
==== Front
Wellcome Open Res
Wellcome Open Res
Wellcome Open Research
2398-502X
F1000 Research Limited London, UK

10.12688/wellcomeopenres.22583.1
Data Note
Articles
The genome sequence of the Mauritius parakeet, Alexandrinus eques (formerly Psittacula eques) (A.Newton & E. Newton, 1876)
[version 1; peer review: 2 approved]

Morales Hernán E. Conceptualization Funding Acquisition Investigation Project Administration Resources Writing – Review & Editing https://orcid.org/0000-0002-2964-020X
12
Groombridge Jim J. Conceptualization Resources Writing – Original Draft Preparation Writing – Review & Editing https://orcid.org/0000-0002-6941-8187
3
Tollington Simon Writing – Original Draft Preparation Writing – Review & Editing 4
Henshaw Sion Writing – Original Draft Preparation Writing – Review & Editing 5
Tatayah Vikash Project Administration Resources Writing – Review & Editing https://orcid.org/0000-0003-0759-254X
5
Ruhomaun Kevin Project Administration Resources Writing – Review & Editing 6
van Oosterhout Cock Conceptualization Writing – Original Draft Preparation Writing – Review & Editing https://orcid.org/0000-0002-5653-738X
7
Gilbert M. Thomas P. Funding Acquisition Project Administration Resources Writing – Review & Editing https://orcid.org/0000-0002-5805-7195
12
Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory teama
Wellcome Sanger Institute Scientific Operations: Sequencing Operations
Wellcome Sanger Institute Tree of Life Core Informatics team
Tree of Life Core Informatics collective
1 Globe Institute, University of Copenhagen, Copenhagen, Denmark
2 Centre for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
3 Durrell Institute of Conservation and Ecology, Division of Human and Social Sciences, University of Kent, Canterbury, England, UK
4 School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Nottingham, England, UK
5 Mauritian Wildlife Foundation, Vacoas, Mauritius
6 National Parks and Conservation Service (Government of Mauritius), Reduit, Mauritius
7 School of Environmental Sciences, University of East Anglia, Norwich, England, UK
a Mark.Blaxter@sanger.ac.uk
No competing interests were disclosed.

16 7 2024
2024
9 37821 6 2024
Copyright: © 2024 Morales HE et al.
2024
https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

We present a genome assembly from an individual male Alexandrinus eques, formerly Psittacula eques (the Mauritius Parakeet; Chordata; Aves; Psittaciformes; Psittacidae). The genome sequence is 1203.8 megabases in span. Most of the assembly is scaffolded into 35 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 18.86 kilobases in length.

Psittacula eques
Psittacula echo
Alexandrinus eques
Mauritius parakeet
genome sequence
chromosomal
Psittaciformes
Royal Society International Collaboration Awards 2020ICA∖R1∖201194 Wellcome Trust218328 206194 Danish National Research FoundationDNRF143 European Union's Horizon 2020 Research and Innovation ProgrammeMarieSklodowska-Curiegrant(840519) European Research CouncilERODE 101078303 This work was supported by Wellcome through core funding to the Wellcome Sanger Institute [206194, <a href=https://doi.org/10.35802/206194>https://doi.org/10.35802/206194</a>]. Danish National Research Foundation grant DNRF143 European Union's Horizon 2020 Research and Innovation Programme under a Marie Sklodowska-Curie grant (840519) European Research Council (ERODE, 101078303) Royal Society International Collaboration Awards 2020 (ICA∖R1∖201194) The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
==== Body
pmcSpecies taxonomy

Eukaryota; Metazoa; Chordata; Aves; Psittaciformes; Psittacidae; Psittacula (NCBI:txid1560315)

Background

The Mauritius Parakeet ( Alexandrinus eques; formerly Psittacula eques) is the only surviving endemic species of parrot in Mauritius and the Mascarenes. Characterised by its bright green plumage and red and black markings around the beak and eyes ( Figure 1A), this parakeet feeds predominantly on the fruits, flowers, and leaves of native forest plants. Mauritius Parakeets are known for nesting in natural cavities within mature trees, where they lay between two to four eggs each breeding season, occurring mainly from September to January.

Figure 1. The fall and rise of the Mauritius Parakeet.

( A) A male Mauritius Parakeet ( Alexandrinus eques; formerly Psittacula eques; photo credit Jacques de Speville) ( B) Demographic trajectory over time (bottleneck and recovery), the line represents the number of known breeding pairs from the monitoring programme. Total population census sizes are estimated to include non-breeding individuals and sub-adults. The bars represent the number of captive-breed individuals released into the free-living population.

The population of the Mauritius Parakeet plummeted due to habitat loss and invasive species, dwindling to just 20 birds by 1986 and facing imminent extinction ( Jones, 1987; Tatayah et al., 2007). Through three decades of dedicated conservation efforts, including captive-breeding, reintroductions, nest management, predator control, supplementary feeding, and habitat restoration, the population rebounded ( Jones, 2010; Jones et al., 2013; Jones et al., 1998) ( Figure 1B). By 2019, it reached an estimated 750 birds, leading to its downlisting in the IUCN Red List from Critically Endangered to Vulnerable ( BirdLife International, 2019).

In 2005, Psittacine Beak and Feather Disease (PBFD) was detected in the population, a condition characterised by feather dystrophy and immunosuppression, of which the causative agent, Beak and Feather Disease Virus, is one of the most common infections of parrots ( Kundu et al., 2012; Ritchie et al., 1989). Although PBFD can be fatal, with juveniles being particularly susceptible ( Todd, 2000), the species continued to recover despite significant sub-lethal effects detected in the free-living population ( Tollington et al., 2015).

During the decline and recovery of the species, there was a significant loss in genetic diversity, including reduced heterozygosity and allelic richness at microsatellite loci ( Tollington et al., 2013). Initial genetic structure showed differentiation between subpopulations, which has diminished as their size and range expanded due to intensive conservation efforts ( Raisin et al., 2012; Tollington et al., 2013). The ongoing conservation management includes supplementary feeding, which boosts reproductive fitness but may increase BFDV transmission ( Fogell et al., 2019; Fogell et al., 2021; Tollington et al., 2019). Continuous monitoring of genetic diversity, viral prevalence, productivity, and population viability is in place. A vast archive of biological samples and decades of fitness data position the Mauritius Parakeet as an ideal model for studying genomic changes during population recovery and during outbreaks of emergent infectious diseases (EID).

Currently, hundreds of whole genomes are being re-sequenced from historical (pre-1900), recent (1990–2000) and contemporary samples to address these questions. This research efforts are part of a collaboration between several universities (UK - University of Kent, University of East Anglia, Denmark - The University of Copenhagen) with the Government of Mauritius’ National Parks and Conservation Service (NPCS) and the Mauritian Wildlife Foundation (MWF – conservation NGO, Mauritius). The conservation monitoring and management of the Mauritius Parakeet is led by the MWF in collaboration with the NPCS under guidance from the university partners. Recent conservation actions have also been implemented by Ebony Forest Reserve (conservation group).

Genome sequence report

The genome was sequenced from a blood sample from a male Alexandrinus eques collected from Black River Gorges, Mauritius (–20.39, 57.45). A total of 79-fold coverage in Pacific Biosciences single-molecule HiFi long reads was generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 41 missing joins or mis-joins, reducing the scaffold number by 13.13%, and increasing the scaffold N50 by 1.02%.

The final assembly has a total length of 1203.8 Mb in 171 sequence scaffolds with a scaffold N50 of 107.0 Mb ( Table 1). The snail plot in Figure 2 provides a summary of the assembly statistics, while the distribution of assembly scaffolds on GC proportion and coverage is shown in Figure 3. The cumulative assembly plot in Figure 4 shows curves for subsets of scaffolds assigned to different phyla. Most (97.61%) of the assembly sequence was assigned to 35 chromosomal-level scaffolds, representing 34 autosomes and the Z sex chromosome. Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size ( Figure 5; Table 2). The Z chromosome was identified based on the Hi-C signal from female sample (Pacbio HiFi data used for de novo assembly was derived from a male). While not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited. The mitochondrial genome was also assembled and can be found as a contig within the multifasta file of the genome submission.

Table 1. Genome data for Alexandrinus eques; formerly Psittacula eques, bPsiEch3.1.

Project accession data	
Assembly identifier	bPsiEch3.1	
Species	Psittacula eques	
Specimen	bPsiEch3	
NCBI taxonomy ID	232653	
BioProject	PRJEB64768	
BioSample ID	SAMEA12361725	
Isolate information	bPsiEch3, male (PacBio DNA and Illumina RNA sequencing)
bPsiEch1, female (Illumina Hi-C sequencing)	
Assembly metrics *	Benchmark	
Consensus quality (QV)	65.6	≥ 50	
k-mer completeness	100.0%	≥ 95%	
BUSCO **	C:97.1%[S:96.8%,D:0.3%],F:0.5%,
M:2.4%,n:8,338	C ≥ 95%	
Percentage of assembly mapped
to chromosomes	97.61%	≥ 95%	
Sex chromosomes	Z	localised homologous pairs	
Organelles	Mitochondrial genome: 18.86 kb	complete single alleles	
Raw data accessions	
PacificBiosciences Sequel IIe,
Revio	ERR11809169, ERR11809168	
Hi-C Illumina	ERR11814144	
PolyA RNA-Seq Illumina	ERR11814145	
Genome assembly	
Assembly accession	GCA_963264785.1	
Accession of alternate haplotype	GCA_963243765.1	
Span (Mb)	1203.8	
Number of contigs	530	
Contig N50 length (Mb)	5.9	
Number of scaffolds	171	
Scaffold N50 length (Mb)	107.0	
Longest scaffold (Mb)	168.07	
* Assembly metric benchmarks are adapted from column VGP-2020 of “Table 1: Proposed standards and metrics for defining genome assembly quality” from Rhie et al. (2021).

** BUSCO scores based on the vertebrata_odb10 BUSCO set using version v5.4.3. C = complete [S = single copy, D = duplicated], F = fragmented, M = missing, n = number of orthologues in comparison. A full set of BUSCO scores is available at https://blobtoolkit.genomehubs.org/view/Psittacula%20echo/dataset/CAUJLS01/busco.

Figure 2. Genome assembly of Alexandrinus eques metrics.

The BlobToolKit snail plot shows N50 metrics and BUSCO gene completeness. The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 1,203,831,919 bp assembly. The distribution of scaffold lengths is shown in dark grey with the plot radius scaled to the longest scaffold present in the assembly (168,074,981 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (106,987,384 and 12,426,226 bp), respectively. The pale grey spiral shows the cumulative scaffold count on a log scale with white scale lines showing successive orders of magnitude. The blue and pale-blue area around the outside of the plot shows the distribution of GC, AT and N percentages in the same bins as the inner plot. A summary of complete, fragmented, duplicated and missing BUSCO genes in the aves_odb10 set is shown in the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Psittacula%20echo/dataset/CAUJLS01/snail.

Figure 3. Genome assembly of Alexandrinus eques; formerly Psittacula eques, bPsiEch3.1: BlobToolKit GC-coverage plot.

Sequences are coloured by phylum. Circles are sized in proportion to sequence length. Histograms show the distribution of sequence length sum along each axis. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Psittacula%20echo/dataset/CAUJLS01/blob.

Figure 4. Genome assembly of Alexandrinus eques; formerly Psittacula eques, bPsiEch3.1: BlobToolKit cumulative sequence plot.

The grey line shows cumulative length for all sequences. Coloured lines show cumulative lengths of sequences assigned to each phylum using the buscogenes taxrule. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Psittacula%20echo/dataset/CAUJLS01/cumulative.

Figure 5. Genome assembly of Alexandrinus eques; formerly Psittacula eques, bPsiEch3.1: Hi-C contact map of the bPsiEch3.1 assembly, visualised using HiGlass.

Chromosomes are shown in order of size from left to right and top to bottom. An interactive version of this figure may be viewed at https://genome-note-higlass.tol.sanger.ac.uk/l/?d=fHq_ahaYS1eLkq54w6IhGA.

Table 2. Chromosomal pseudomolecules in the genome assembly of Alexandrinus eques; formerly Psittacula eques, bPsiEch3.

INSDC
accession	Chromosome	Length
(Mb)	GC%	
OY725420.1	1	168.07	41.0	
OY725421.1	2	161.94	40.5	
OY725422.1	3	128.36	40.5	
OY725423.1	4	122.79	41.0	
OY725425.1	5	90.32	42.5	
OY725426.1	6	79.82	41.0	
OY725427.1	7	66.74	42.0	
OY725428.1	8	24.68	44.5	
OY725429.1	9	23.83	43.5	
OY725430.1	10	22.8	43.5	
OY725431.1	11	21.18	45.0	
OY725432.1	12	17.15	46.0	
OY725433.1	13	15.5	45.5	
OY725434.1	14	13.94	47.5	
OY725435.1	15	12.76	47.5	
OY725436.1	16	12.43	48.0	
OY725437.1	17	8.98	48.5	
OY725438.1	18	7.91	49.0	
OY725439.1	19	7.9	53.0	
OY725440.1	20	7.85	45.5	
OY725441.1	21	7.78	51.5	
OY725442.1	22	7.5	52.0	
OY725443.1	23	6.57	53.0	
OY725444.1	24	6.49	53.5	
OY725445.1	25	6.37	50.5	
OY725446.1	26	4.64	56.0	
OY725447.1	27	4.27	57.0	
OY725448.1	28	2.76	59.0	
OY725449.1	29	2.47	56.0	
OY725450.1	30	1.41	59.0	
OY725451.1	31	1.11	57.5	
OY725452.1	32	0.49	60.5	
OY725453.1	33	0.48	58.5	
OY725454.1	34	0.23	61.5	
OY725424.1	Z	106.99	41.0	
OY725455.1	MT	0.02	46.0	

The estimated Quality Value (QV) of the final assembly is 65.6 with k-mer completeness of 100.0%, and the assembly has a BUSCO v5.4.3 completeness of 97.1% (single = 96.8%, duplicated = 0.3%), using the vertebrata_odb10 reference set ( n = 8,338).

Metadata for specimens, BOLD barcode results, spectra estimates, sequencing runs, contaminants and pre-curation assembly statistics are given at https://links.tol.sanger.ac.uk/species/232653.

Methods

Sample acquisition and nucleic acid extraction

Blood sampling of Mauritius Parakeets is routinely conducted by the MWF and university researchers, overseen by the International Zoo Veterinary Group (IZVG). Samples are taken from the jugular and brachial veins of chicks at 45 days old in their nests and from adults captured at nest sites or field aviaries during health checks. Extensive blood sampling has been performed throughout the species’ restoration, with most chicks and some adults sampled opportunistically. For genomic sequencing, blood from select individuals was preserved in absolute ethanol and immediately frozen to minimize DNA degradation. The genome and RNA was sequenced from a male bird (specimen ID SAN1100033, ToLID bPsiEch3) caught in the field aviary on 2020-01-15, while a female specimen (specimen ID SAN1100031, ToLID bPsiEch1) collected on 2020-01-29 was used for Hi-C sequencing.

The workflow for high molecular weight (HMW) DNA extraction at the Wellcome Sanger Institute (WSI) Tree of Life Core Laboratory includes a sequence of core procedures: sample preparation; sample homogenisation, DNA extraction, fragmentation, and clean-up. In sample preparation, the bPsiEch3 sample was weighed and kept on dry ice ( Jay et al., 2023). For sample homogenisation, blood was cryogenically disrupted using the Covaris cryoPREP ® Automated Dry Pulverizer ( Narváez-Gómez et al., 2023). HMW DNA was extracted using the manual Nucleated Blood Nanobind ® protocol ( Denton et al., 2023a). DNA was sheared into an average fragment size of 12–20 kb in a Megaruptor 3 system with speed setting 31 ( Bates et al., 2023). Sheared DNA was purified by solid-phase reversible immobilisation ( Strickland et al., 2023). The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer and Qubit Fluorometer and Qubit dsDNA High Sensitivity Assay kit. Fragment size distribution was evaluated by running the sample on the FemtoPulse system.

RNA was extracted from the bPsiEch3 blood sample in the Tree of Life Laboratory at the WSI using the RNA Extraction: Automated MagMax™ mirVana protocol ( do Amaral et al., 2023). The RNA concentration was assessed using a Nanodrop spectrophotometer and a Qubit Fluorometer using the Qubit RNA Broad-Range Assay kit. Analysis of the integrity of the RNA was done using the Agilent RNA 6000 Pico Kit and Eukaryotic Total RNA assay.

Protocols developed by the WSI Tree of Life laboratory are publicly available on protocols.io ( Denton et al., 2023b).

Sequencing

Pacific Biosciences HiFi circular consensus DNA sequencing libraries were constructed according to the manufacturers’ instructions. Poly(A) RNA-Seq libraries were constructed using the NEB Ultra II RNA Library Prep kit. DNA and RNA sequencing was performed by the Scientific Operations core at the WSI on Pacific Biosciences Sequel IIe, Revio (HiFi) and Illumina NovaSeq 6000 (RNA-Seq) instruments. Hi-C data were also generated from blood from bPsiEch1 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.

Genome assembly and curation

Assembly was carried out with Hifiasm ( Cheng et al., 2021) and haplotypic duplication was identified and removed with purge_dups ( Guan et al., 2020). The assembly was then scaffolded with Hi-C data ( Rao et al., 2014) using YaHS ( Zhou et al., 2023). The assembly was checked for contamination and corrected using the TreeVal pipeline ( Pointon et al., 2023). Manual curation was performed using JBrowse2 ( Diesh et al., 2023), HiGlass ( Kerpedjiev et al., 2018) and PretextView ( Harry, 2022). The mitochondrial genome was assembled using MitoHiFi ( Uliano-Silva et al., 2023), which runs MitoFinder ( Allio et al., 2020) or MITOS ( Bernt et al., 2013) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.

Final assembly evaluation

The final assembly was post-processed and evaluated with the three Nextflow ( Di Tommaso et al., 2017) DSL2 pipelines “sanger-tol/readmapping” ( Surana et al., 2023a), “sanger-tol/genomenote” ( Surana et al., 2023b), and “sanger-tol/blobtoolkit” ( Muffato et al., 2024). The pipeline sanger-tol/readmapping aligns the Hi-C reads with bwa-mem2 ( Vasimuddin et al., 2019) and combines the alignment files with SAMtools ( Danecek et al., 2021). The sanger-tol/genomenote pipeline transforms the Hi-C alignments into a contact map with BEDTools ( Quinlan & Hall, 2010) and the Cooler tool suite ( Abdennur & Mirny, 2020), which is then visualised with HiGlass ( Kerpedjiev et al., 2018). It also provides statistics about the assembly with the NCBI datasets ( Sayers et al., 2024) report, computes k-mer completeness and QV consensus quality values with FastK and MerquryFK, and a completeness assessment with BUSCO ( Manni et al., 2021).

The sanger-tol/blobtoolkit pipeline is a Nextflow port of the previous Snakemake Blobtoolkit pipeline ( Challis et al., 2020). It aligns the PacBio reads with SAMtools and minimap2 ( Li, 2018) and generates coverage tracks for regions of fixed size. In parallel, it queries the GoaT database ( Challis et al., 2023) to identify all matching BUSCO lineages to run BUSCO ( Manni et al., 2021). For the three domain-level BUSCO lineage, the pipeline aligns the BUSCO genes to the Uniprot Reference Proteomes database ( Bateman et al., 2023) with DIAMOND ( Buchfink et al., 2021) blastp. The genome is also split into chunks according to the density of the BUSCO genes from the closest taxonomically lineage, and each chunk is aligned to the Uniprot Reference Proteomes database with DIAMOND blastx. Genome sequences that have no hit are then chunked with seqtk and aligned to the NT database with blastn ( Altschul et al., 1990). All those outputs are combined with the blobtools suite into a blobdir for visualisation.

All three pipelines were developed using the nf-core tooling ( Ewels et al., 2020), use MultiQC ( Ewels et al., 2016), and make extensive use of the Conda package manager, the Bioconda initiative ( Grüning et al., 2018), the Biocontainers infrastructure ( da Veiga Leprevost et al., 2017), and the Docker ( Merkel, 2014) and Singularity ( Kurtzer et al., 2017) containerisation solutions.

Table 3 contains a list of relevant software tool versions and sources.

Table 3. Software tools: versions and sources.

Software tool	Version	Source	
BEDTools	2.30.0	https://github.com/arq5x/bedtools2	
Blast	2.14.0	ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/	
BlobToolKit	4.3.7	https://github.com/blobtoolkit/blobtoolkit	
BUSCO	5.4.3	https://gitlab.com/ezlab/busco	
BUSCO	5.4.3 and 5.5.0	https://gitlab.com/ezlab/busco	
bwa-mem2	2.2.1	https://github.com/bwa-mem2/bwa-mem2	
Cooler	0.8.11	https://github.com/open2c/cooler	
DIAMOND	2.1.8	https://github.com/bbuchfink/diamond	
fasta_windows	0.2.4	https://github.com/tolkit/fasta_windows	
FastK	427104ea91c78c3b8b8b49f1a7d6bbeaa869ba1c	https://github.com/thegenemyers/FASTK	
GoaT CLI	0.2.5	https://github.com/genomehubs/goat-cli	
Hifiasm	0.16.1-r375	https://github.com/chhylp123/hifiasm	
HiGlass	1.11.6	https://github.com/higlass/higlass	
HiGlass	44086069ee7d4d3f6f3f0012569789ec138f42b84aa44357826c0b6753eb28de	https://github.com/higlass/higlass	
MerquryFK	d00d98157618f4e8d1a9190026b19b471055b22e	https://github.com/thegenemyers/MERQURY.FK	
MitoHiFi	2	https://github.com/marcelauliano/MitoHiFi	
MultiQC	1.14, 1.17, and 1.18	https://github.com/MultiQC/MultiQC	
NCBI Datasets	15.12.0	https://github.com/ncbi/datasets	
Nextflow	23.04.0-5857	https://github.com/nextflow-io/nextflow	
PretextView	0.2	https://github.com/wtsi-hpag/PretextView	
purge_dups	1.2.3	https://github.com/dfguan/purge_dups	
samtools	1.16.1, 1.17, and 1.18	https://github.com/samtools/samtools	
sanger-tol/genomenote	1.1.1	https://github.com/sanger-tol/genomenote	
sanger-tol/readmapping	1.2.1	https://github.com/sanger-tol/readmapping	
Seqtk	1.3	https://github.com/lh3/seqtk	
Singularity	3.9.0	https://github.com/sylabs/singularity	
TreeVal	1.0.0	https://github.com/sanger-tol/treeval	
YaHS	yahs-1.1.91eebc2	https://github.com/c-zhou/yahs	

Wellcome Sanger Institute – Legal and Governance

The materials that have contributed to this genome note have been supplied by a Tree of Life collaborator. The Wellcome Sanger Institute employs a process whereby due diligence is carried out proportionate to the nature of the materials themselves, and the circumstances under which they have been/are to be collected and provided for use. The purpose of this is to address and mitigate any potential legal and/or ethical implications of receipt and use of the materials as part of the research project, and to ensure that in doing so we align with best practice wherever possible.

The overarching areas of consideration are:

•      Ethical review of provenance and sourcing of the material

•      Legality of collection, transfer and use (national and international)

Each transfer of samples is undertaken according to a Research Collaboration Agreement or Material Transfer Agreement entered into by the Tree of Life collaborator, Genome Research Limited (operating as the Wellcome Sanger Institute) and in some circumstances other Tree of Life collaborators.

Acknowledgements

We thank Houshna Naujeer and colleagues at the National Parks and Conservation Service, Government of Mauritius, for support and permits for sample collection. We are grateful with Carl Jones and Deborah De Chazal for their roles in the Mauritius Parakeet conservation programme.

Data availability

European Nucleotide Archive: Psittacula echo (Mauritius parakeet). Accession number PRJEB64768; https://identifiers.org/ena.embl/PRJEB64768 ( Wellcome Sanger Institute, 2023). The genome sequence is released openly for reuse. The Psittacula eques genome sequencing initiative is part of the Vertebrate Genomes Project. All raw sequence data and the assembly have been deposited in INSDC databases. The genome will be annotated using available RNA-Seq data and presented through the Ensembl pipeline at the European Bioinformatics Institute. Raw data and assembly accession identifiers are reported in Table 1.

Author information

Members of the Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team are listed here: https://doi.org/10.5281/zenodo.10066175.

Members of Wellcome Sanger Institute Scientific Operations: Sequencing Operations are listed here: https://doi.org/10.5281/zenodo.10043364.

Members of the Wellcome Sanger Institute Tree of Life Core Informatics team are listed here: https://doi.org/10.5281/zenodo.10066637.

Members of the Tree of Life Core Informatics collective are listed here: https://doi.org/10.5281/zenodo.5013541.

10.21956/wellcomeopenres.24881.r94859
Reviewer response for version 1
Wold Jana 1Referee https://orcid.org/0000-0001-8095-4282

1 University of Canterbury, Christchurch, New Zealand
18 9 2024 Copyright: © 2024 Wold J
2024
https://creativecommons.org/licenses/by/4.0/ This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Version 1recommendationapprove
Here, Morales et al provide a high quality genome assembly for a threatened parrot. This assembly will become a foundational genomic resource for a investigation into the genomic diversity of the Mauritius Parakeet. The assembly, and RNA-seq informed annotation, and may be a powerful tool in the continued conservation efforts for this species.

The methods implemented here are well considered and appropriate. I have full confidence that the assembly will be a useful resource going forward.

Are sufficient details of methods and materials provided to allow replication by others?

Yes

Is the rationale for creating the dataset(s) clearly described?

Yes

Are the datasets clearly presented in a useable and accessible format?

Yes

Are the protocols appropriate and is the work technically sound?

Yes

Reviewer Expertise:

Conservation genomics

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

10.21956/wellcomeopenres.24881.r94861
Reviewer response for version 1
Fuchs Jérôme 1Referee
1 Institut de Systématique Evolution Biodiversité, Muséum national d'Histoire naturelle CNRS SU EPHE UA, Paris, France
5 9 2024 Copyright: © 2024 Fuchs J
2024
https://creativecommons.org/licenses/by/4.0/ This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Version 1recommendationapprove
The following manuscript describes a chromosome level assembly of the endemic Mauritius parakeet Alexandrinus equees, a species that went through a very strong population bottleneck

Maybe it is worth mentionning that, as currently understood, the Mauritius Parakeet is nested within or very closely related to the Ring-necked Parakeet (A. krameri)

I have very few comments that the authors may consider.

"Most of the assembly sequence was assigned to 35 pseudomolecules, representing 34 autosomes and the Z sex chromosome."

2n= 70 is coherent with what is known for Alexandrinus species (Ray-Chaudhuri et al. 1969), although not identical to its sister species; maybe worth mentioning somewhere in the manuscript

Note that on Genbank, the genome project is for Psittacula echo, which is the endemic subspecies to Mauritius. It may be worth to homogenize the names between Genbank and the present manuscript, either by using Alexandrinus eques echo throughout the manuscript and mention that the extinct nominate subspecies is found on Reunion Is or change the name on genbank.

As part of a genome description publication, it may be useful to further comparative analyses have the proportion of: The percentage of repeat sequences

Number of protein coding genes (since RNA was sequenced)

and possibly:  Number of snps in the genome and per chromosome

The two former descriptive statistics are routinely mentioned in genome papers

Are sufficient details of methods and materials provided to allow replication by others?

Yes

Is the rationale for creating the dataset(s) clearly described?

Yes

Are the datasets clearly presented in a useable and accessible format?

Yes

Are the protocols appropriate and is the work technically sound?

Yes

Reviewer Expertise:

Molecular Systematics, Genomics

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

Competing interests: No competing interests were disclosed.

Competing interests: No competing interests were disclosed.
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